ReactionSystems/src/rsprocess/structure.rs

#![allow(dead_code)]

use std::collections::{BTreeSet, HashMap, VecDeque};
use std::hash::Hash;
use std::rc::Rc;
use super::translator::{IdType};

// -----------------------------------------------------------------------------
// RSset
// -----------------------------------------------------------------------------
#[derive(Clone, Debug, PartialEq, Eq, PartialOrd, Ord, Hash)]
pub struct RSset {
    identifiers: BTreeSet<IdType>
}

impl<const N: usize> From<[IdType; N]> for RSset {
    fn from(arr: [IdType; N]) -> Self {
	RSset{identifiers: BTreeSet::from(arr)}
    }
}

impl From<&[IdType]> for RSset {
    fn from(arr: &[IdType]) -> Self {
	RSset{identifiers: BTreeSet::from_iter(arr.to_vec())}
    }
}

impl From<Vec<IdType>> for RSset {
    fn from(arr: Vec<IdType>) -> Self {
	RSset{identifiers: BTreeSet::from_iter(arr)}
    }
}

impl RSset {
    pub fn new() -> Self {
	RSset{identifiers: BTreeSet::new()}
    }

    pub fn is_subset(&self, b: &RSset) -> bool {
	self.identifiers.is_subset(&b.identifiers)
    }

    pub fn is_disjoint(&self, b: &RSset) -> bool {
	self.identifiers.is_disjoint(&b.identifiers)
    }

    pub fn union(&self, b: &RSset) -> RSset {
	// TODO maybe find more efficient way without copy/clone
	let mut ret: RSset = b.clone();
	ret.identifiers.extend(self.identifiers.iter());
	ret
    }

    pub fn union_option(&self, b: Option<&RSset>) -> RSset {
	if let Some(b) = b {
	    self.union(b)
	} else {
	    self.clone()
	}
    }

    pub fn intersection(&self, b: &RSset) -> RSset {
	// TODO maybe find more efficient way without copy/clone
	let res: BTreeSet<_> = b.identifiers.intersection(&self.identifiers)
					   .copied()
					   .collect();
	RSset { identifiers: res }
    }

    pub fn subtraction(&self, b: &RSset) -> RSset {
	// TODO maybe find more efficient way without copy/clone
	let res: BTreeSet<_> = self.identifiers.difference(&b.identifiers)
					      .copied()
					      .collect();
	RSset { identifiers: res }
    }

    pub fn set(&self) -> &BTreeSet<IdType> {
	&self.identifiers
    }

    pub fn iter(&self) -> std::collections::btree_set::Iter<'_, IdType> {
	self.identifiers.iter()
    }

    pub fn len(&self) -> usize {
	self.identifiers.len()
    }

    pub fn insert(&mut self, el: IdType) -> bool {
	self.identifiers.insert(el)
    }

    pub fn push(&mut self, b: &RSset) {
	self.identifiers.extend(b.iter())
    }
}

impl Default for RSset {
    fn default() -> Self {
	RSset::new()
    }
}

impl IntoIterator for RSset {
    type Item = IdType;
    type IntoIter = std::collections::btree_set::IntoIter<Self::Item>;

    fn into_iter(self) -> Self::IntoIter {
	self.identifiers.into_iter()
    }
}


// -----------------------------------------------------------------------------
// RSreaction
// -----------------------------------------------------------------------------
#[derive(Clone, Debug)]
pub struct RSreaction {
    reactants: RSset,
    inihibitors: RSset,
    products: RSset
}

impl RSreaction {
    pub fn new() -> Self {
	RSreaction{ reactants:   RSset::new(),
		    inihibitors: RSset::new(),
		    products:    RSset::new(), }
    }

    pub fn from(reactants: RSset, inihibitors: RSset, products: RSset) -> Self {
	RSreaction{ reactants,
		    inihibitors,
		    products }
    }

    // see enable
    pub fn enabled(&self, current_state: &RSset) -> bool {
	self.reactants.is_subset(current_state)
	    && self.inihibitors.is_disjoint(current_state)
    }

    pub fn products_clone(&self) -> RSset {
	self.products.clone()
    }

    pub fn reactants(&self) -> &RSset {
	&self.reactants
    }

    pub fn inihibitors(&self) -> &RSset {
	&self.inihibitors
    }

    pub fn products(&self) -> &RSset {
	&self.products
    }
}

impl Default for RSreaction {
    fn default() -> Self {
	RSreaction::new()
    }
}



// -----------------------------------------------------------------------------
// RSprocess
// -----------------------------------------------------------------------------
#[derive(Clone, Debug)]
pub enum RSprocess {
    Nill,
    RecursiveIdentifier{ identifier: IdType },
    EntitySet{ entities: RSset,
	       next_process: Rc<RSprocess> },
    WaitEntity{ repeat: i64,
		repeated_process: Rc<RSprocess>,
		next_process: Rc<RSprocess> },
    Summation{ children: Vec<Rc<RSprocess>> },
    NondeterministicChoice{ children: Vec<Rc<RSprocess>> }
}

impl RSprocess {
    // TODO: remove all the clone()
    pub fn concat(&self, new: &RSprocess) -> RSprocess{
	match (self, new) {
	    (RSprocess::NondeterministicChoice{children: c1},
	     RSprocess::NondeterministicChoice{children: c2}) => {
		RSprocess::NondeterministicChoice {
		    children: [c1.clone(),
			       c2.clone()].concat()
		}
	    },
	    (RSprocess::NondeterministicChoice{children}, new) |
	    (new, RSprocess::NondeterministicChoice{children}) => {
		let mut new_children = children.clone();
		new_children.push(Rc::new(new.clone()));
		RSprocess::NondeterministicChoice{ children: new_children }
	    },
	    (_, _) => {
		RSprocess::NondeterministicChoice {
		    children: vec![Rc::new(self.clone()),
				   Rc::new(new.clone())]
		}
	    }
	}
    }

    pub fn all_elements(&self) -> RSset {
	let mut queue = VecDeque::from([self]);
	let mut elements = RSset::new();

	while let Some(el) = queue.pop_front() {
	    match el {
		Self::Nill => {}
		Self::RecursiveIdentifier { identifier: _ } => {}
		Self::EntitySet { entities, next_process } => {
		    elements.push(entities);
		    queue.push_back(next_process);
		}
		Self::WaitEntity { repeat: _, repeated_process, next_process } => {
		    queue.push_back(repeated_process);
		    queue.push_back(next_process);
		}
		Self::Summation { children } => {
		    for c in children {
			queue.push_back(c);
		    }
		}
		Self::NondeterministicChoice { children } => {
		    for c in children {
			queue.push_back(c);
		    }
		}
	    }
	}
	elements
    }
}

// -----------------------------------------------------------------------------
// RSchoices
// -----------------------------------------------------------------------------
#[derive(Clone, Debug)]
pub struct RSchoices {
    context_moves: Vec<(Rc<RSset>, Rc<RSprocess>)>
}

impl RSchoices {
    pub fn new() -> Self {
	RSchoices{ context_moves: vec![] }
    }

    pub fn new_not_empty() -> Self {
	RSchoices{ context_moves: vec![(Rc::new(RSset::new()),
					Rc::new(RSprocess::Nill))] }
    }

    pub fn append(&mut self, a: &mut RSchoices) {
	self.context_moves.append(&mut a.context_moves);
    }

    pub fn replace(&mut self, a: Rc<RSprocess>) {
	self.context_moves =
	    self.context_moves
	    .iter_mut()
	    .map(|(c1, _)| (Rc::clone(c1), Rc::clone(&a))).collect::<Vec<_>>();
    }

    pub fn shuffle(&mut self, choices: RSchoices) {
	match (self.context_moves.is_empty(), choices.context_moves.is_empty()){
	    (true, true) => {}
	    (true, false) => { self.context_moves = choices.context_moves }
	    (false, true) => {}
	    (false, false) => {
		let mut new_self = vec![];
		for item_self in &self.context_moves {
		    for item_choices in &choices.context_moves {
			new_self.push(
			    (Rc::new(item_self.0.union(&item_choices.0)),
			     Rc::new(item_self.1.concat(&item_choices.1)))
			);
		    }
		}
		self.context_moves = new_self;
	    }
	}
    }

    pub fn iter(&self) -> std::slice::Iter<'_, (Rc<RSset>, Rc<RSprocess>)> {
	self.context_moves.iter()
    }
}

impl IntoIterator for RSchoices {
    type Item = (Rc<RSset>, Rc<RSprocess>);
    type IntoIter = std::vec::IntoIter<Self::Item>;

    fn into_iter(self) -> Self::IntoIter {
	self.context_moves.into_iter()
    }
}


impl<const N: usize> From<[(Rc<RSset>, Rc<RSprocess>); N]> for RSchoices {
    fn from(arr: [(Rc<RSset>, Rc<RSprocess>); N]) -> Self {
	RSchoices{context_moves: arr.to_vec()}
    }
}

impl From<&[(Rc<RSset>, Rc<RSprocess>)]> for RSchoices {
    fn from(arr: &[(Rc<RSset>, Rc<RSprocess>)]) -> Self {
	RSchoices{context_moves: arr.to_vec()}
    }
}

impl From<Vec<(Rc<RSset>, Rc<RSprocess>)>> for RSchoices {
    fn from(arr: Vec<(Rc<RSset>, Rc<RSprocess>)>) -> Self {
	RSchoices{context_moves: arr}
    }
}

// -----------------------------------------------------------------------------
// RSenvironment
// -----------------------------------------------------------------------------
#[derive(Clone, Debug)]
pub struct RSenvironment {
    definitions: HashMap<IdType, RSprocess>,
}

impl RSenvironment {
    pub fn new() -> RSenvironment {
	RSenvironment{definitions: HashMap::new()}
    }

    pub fn get(&self, k: IdType) -> Option<&RSprocess> {
	self.definitions.get(&k)
    }

    pub fn iter(&self) -> std::collections::hash_map::Iter<'_, u32, RSprocess> {
	self.definitions.iter()
    }

    pub fn all_elements(&self) -> RSset {
	let mut acc = RSset::new();
	for (_, process) in self.definitions.iter() {
	    acc.push(&process.all_elements());
	}
	acc
    }
}

impl Default for RSenvironment {
    fn default() -> Self {
	RSenvironment::new()
    }
}

impl<const N: usize> From<[(IdType, RSprocess); N]> for RSenvironment {
    fn from(arr: [(IdType, RSprocess); N]) -> Self {
	RSenvironment{definitions: HashMap::from(arr)}
    }
}

impl From<&[(IdType, RSprocess)]> for RSenvironment {
    fn from(arr: &[(IdType, RSprocess)]) -> Self {
	RSenvironment{definitions: HashMap::from_iter(arr.to_vec())}
    }
}

impl From<Vec<(IdType, RSprocess)>> for RSenvironment {
    fn from(arr: Vec<(IdType, RSprocess)>) -> Self {
	RSenvironment{definitions: HashMap::from_iter(arr)}
    }
}

// -----------------------------------------------------------------------------
// RSsystem
// -----------------------------------------------------------------------------
#[derive(Clone, Debug)]
pub struct RSsystem {
    delta: Rc<RSenvironment>,
    available_entities: RSset,
    context_process: RSprocess,
    reaction_rules: Rc<Vec<RSreaction>>,
}

impl RSsystem {
    pub fn new() -> RSsystem {
	RSsystem {
	    delta: Rc::new(RSenvironment::new()),
	    available_entities: RSset::new(),
	    context_process: RSprocess::Nill,
	    reaction_rules: Rc::new(vec![]),
	}
    }

    pub fn from(delta: Rc<RSenvironment>,
		available_entities: RSset,
		context_process: RSprocess,
		reaction_rules: Rc<Vec<RSreaction>>) -> RSsystem {
	RSsystem { delta: Rc::clone(&delta),
		   available_entities,
		   context_process,
		   reaction_rules: Rc::clone(&reaction_rules) }
    }

    pub fn get_delta(&self) -> &Rc<RSenvironment> {
	&self.delta
    }

    pub fn get_available_entities(&self) -> &RSset {
	&self.available_entities
    }

    pub fn get_context_process(&self) -> &RSprocess {
	&self.context_process
    }

    pub fn get_reaction_rules(&self) -> &Rc<Vec<RSreaction>> {
	&self.reaction_rules
    }
}

impl Default for RSsystem {
    fn default() -> Self {
	RSsystem::new()
    }
}

// -----------------------------------------------------------------------------
// RSsystem
// -----------------------------------------------------------------------------
#[derive(Clone, Debug)]
pub struct RSlabel {
    pub available_entities: RSset,
    pub context: RSset,
    pub t: RSset, ///      union of available_entities and context
    pub reactants: RSset,
    pub reactantsi: RSset, // reactants absent
    pub inihibitors: RSset,
    pub ireactants: RSset, // inhibitors present
    pub products: RSset,
}

impl RSlabel {
    pub fn new() -> Self {
	RSlabel { available_entities: RSset::new(),
		  context: RSset::new(),
		  t: RSset::new(),
		  reactants: RSset::new(),
		  reactantsi: RSset::new(),
		  inihibitors: RSset::new(),
		  ireactants: RSset::new(),
		  products: RSset::new() }
    }

    #[allow(clippy::too_many_arguments)]
    pub fn from(available_entities: RSset,
		context: RSset,
		t: RSset,
		reactants: RSset,
		reactantsi: RSset,
		inihibitors: RSset,
		ireactants: RSset,
		products: RSset,) -> Self {
	RSlabel { available_entities,
		  context,
		  t,
		  reactants,
		  reactantsi,
		  inihibitors,
		  ireactants,
		  products }
    }

    pub fn get_context(&self) -> (RSset, RSset, RSset) {
	// TODO remove clone?
	(self.available_entities.clone(), self.context.clone(), self.t.clone())
    }
}


// -----------------------------------------------------------------------------
// RSassertOp
// -----------------------------------------------------------------------------
#[derive(Clone, Debug)]
pub enum RSassertOp {
    InW,
    InR,
    InI,
    InP
}

// -----------------------------------------------------------------------------
// RSassert
// -----------------------------------------------------------------------------
#[derive(Clone, Debug)]
pub enum RSassert {
    Not(Box<RSassert>),
    Xor(Box<RSassert>, Box<RSassert>),
    Or(Vec<RSassert>),
    And(Vec<RSassert>),
    Sub(RSset, RSassertOp),
    NonEmpty(RSassertOp)
}

// -----------------------------------------------------------------------------
// RSBHML
// -----------------------------------------------------------------------------
#[derive(Clone, Debug)]
#[allow(clippy::upper_case_acronyms)]
pub enum RSBHML {
    True,
    False,
    Or(Vec<RSBHML>),
    And(Vec<RSBHML>),
    Diamond(Box<RSassert>, Box<RSBHML>),
    Box(Box<RSassert>, Box<RSBHML>)
}